Lots of good ideas here. This is my take:

Get a bunch of Velcro cable ties. Start grouping things together. As you go, you’re going to get better placement ideas. Once everything is organized, you can decide the next step. Personally, I would look at having the PC in the bookshelf, and look for a way to put the cables in the wall.

If you do that, I’d suggest having 2 cable runs with a string looping through so that when you change things up you can easily pull a new cable.